Add self only flag

[mcampbell]

Human

Add a --self-only mode for when you want to keep this out of it. In a corporate environment, very often these sorts of tools are "self-only", and they don't want the artifacts in the official repo.

• Uses .git/info/exclude for "personal" git ignoreing
• Will not change or overwrite if filetree was init'd with normal mode
• adds an uninstall which only undoes what it did
• code-reviewed by hand, and with opus 4.8 with a specific prompt for security issues (fixed in later commits; see also)

Spec'd with /grill-me (included).

LLM

Summary

Introduces a self-only mode for users who want the filetree skill installed in a repo without committing its artifacts (CLAUDE.md, AGENTS.md, FILETREE.md) to git. Two new subcommands manage the lifecycle:

• self-only-enable — refuses if target paths are already tracked, appends them to .git/info/exclude (local-only, never touches .gitignore), sets self_only: true in .filetree.json, and records state in .filetree.local.json for reversal.
• self-only-uninstall — surgically removes only the exclude lines this tool added (preserving order, blanks, comments), sets self_only: false, and deletes the state file.

What changed

New: skills/filetree/scripts/filetree_state.py

• State dataclass with exclude_lines field, persisted to .filetree.local.json (not committed).
• load_state / save_state / delete_state with atomic writes and sys.exit error handling.

filetree.py

• cmd_self_only_enable(): validates .git/info isn't a symlink attack, appends target + .local.md variant paths to exclude, preserves unknown config keys on rewrite.
• cmd_self_only_uninstall(): reads exclude lines preserving order/blanks/comments, removes only exact lines recorded in state, preserves unknown config keys.
• CLI: self-only-enable / self-only-uninstall subcommands.

filetree_config.py

• Config.self_only: bool = False field, validated on load.
• tracked_paths(): returns git-tracked files (excluding submodule gitlinks), used by enable to refuse if targets are already tracked.

commands/init.md

• Self-only check: skip CLAUDE.md/AGENTS.md wiring when self_only: true.

Design decisions

• State is a Memento with one field. exclude_lines is the only state recorded — it's everything enable adds that uninstall must reverse. Earlier drafts carried created_files/managed_outputs for .local.md cleanup, but local-file creation is agent-driven (per init.md) and those fields were never populated by any code path. Removed as speculative machinery (YAGNI).
• Surgical exclude edits. Uninstall removes only the exact lines recorded in state, preserving user's existing order, blank lines, and comments. No set-based rewrite.
• Config preserves unknown keys. Both enable and uninstall load raw JSON, set/unset only self_only, and write back — future keys survive.
• Path validation where it matters. .git/info symlink check guards the one filesystem write in enable. Removed misdirected manifest_path validation from wire_local_markdown (the function was deleted — dead code with zero callers).

Testing

• 179 tests pass (uv run --with pytest python -m pytest tests/ -q).
• 6 new tests for self-only-enable (git-required, refuse-if-tracked, exclude-append, config-flag, state-record, summary).
• 5 new tests for self-only-uninstall (git-required, noop-if-not-self-only, removes-exclude-lines, clears-flag, deletes-state).
• 4 new tests for filetree_state.py (path, load-defaults, parse-existing, save, dataclass-defaults).
• 4 new tests for tracked_paths() (empty, staged, committed, gitlinks-excluded).
• Weak/vacuous assertions from initial draft fixed: or to and on exclude-line removal; missing assert result is None on absent-file skip.
• Duplicate TestSelfOnlyEnable class (shadowed 4 tests) deleted.
• E2E verified: enable in scratch repo, state recorded, uninstall, exclude lines removed cleanly, comments preserved, config updated, state file gone.

Files changed

File	Change
commands/init.md	Self-only mode check before wiring step
skills/filetree/scripts/filetree.py	cmd_self_only_enable / cmd_self_only_uninstall + CLI wiring
skills/filetree/scripts/filetree_config.py	self_only config field, tracked_paths()
skills/filetree/scripts/filetree_state.py	New: state persistence module
tests/conftest.py	Load sibling modules
tests/test_filetree.py	Enable/uninstall test suites
tests/test_filetree_config.py	self_only config + tracked_paths tests
tests/test_filetree_state.py	New: state module tests

8 files, +484 / -5.

grill-me session:

Context

Goal: --self-only mode where none of this ever gets committed — new files
go through .git/info/exclude instead of tracked .gitignore, CLAUDE.md
changes go to CLAUDE.local.md instead, and an uninstall removes only what
self-only added.

Q1: Persistence

Persist self_only: true in .filetree.json (mirrors commit_guard). Every
future command reads it, no need to re-pass --self-only.
A: yes, persist it.

Q2: What gets excluded

All three generated files (FILETREE.md, FILETREE.hash.json, .filetree.json)
go into .git/info/exclude in self-only mode — including .filetree.json since
it now carries the personal self_only:true choice.
A: yes, exclude all three.

Q3: CLAUDE.md vs AGENTS.md wiring (revised)

Treat WIRE_FILES generically: CLAUDE.md -> CLAUDE.local.md AND
AGENTS.md -> AGENTS.local.md, both wired in self-only mode (even though
AGENTS.local.md isn't a convention any tool reads yet — future-proofing /
non-Claude-specific).
A: wire both, ensure deterministically removable on uninstall.

Q4: Tracking state for deterministic uninstall

Add .filetree.local.json (git-excluded) recording: git-exclude lines added,
whether CLAUDE.local.md/AGENTS.local.md were freshly created vs pre-existing,
and self-only-managed output files.
A: yes, add state file.

Q4b: Marker gates vs state-file-only for CLAUDE.local.md/AGENTS.local.md text removal

Compared HTML comment markers around the wired
section vs relying purely on state-file-stored text/heading regex.
A: markers — more robust to hand-edits, no need to store injected text
verbatim. Scope to self-only path only (don't retrofit normal-mode wiring's
existing heading-regex idempotency check). Heavily comment the why.

Q6: Uninstall scope

/filetree:uninstall only handles self-only teardown; errors/no-ops if
self_only isn't set. Normal-mode unwind is out of scope.
A: yes, self-only-only for now.

Q7: Retrofitting an already-tracked install

.git/info/exclude has no effect on already-tracked files. If manifest_path /
hash sidecar / .filetree.json are already git ls-files-tracked when
--self-only is invoked, detect and refuse with a clear message (tell user to
git rm --cached first) rather than silently adding no-op exclude lines.
A: yes, refuse with clear message.

Resolved design summary

• --self-only flag on /filetree:init, persists as self_only:true in
  .filetree.json (which is itself self-only-managed).
• .git/info/exclude gets entries for: manifest_path, its hash sidecar,
  .filetree.json, .filetree.local.json, and any of CLAUDE.local.md /
  AGENTS.local.md WE created fresh (not pre-existing ones).
• Refuse to enable self-only if any of those paths are already
  git-tracked (git ls-files check) — clear error, no silent no-op.
• Wiring: generic WIRE_FILES {name}.md -> {name}.local.md for both
  CLAUDE.md and AGENTS.md when self-only. Section wrapped in / markers (self-only path only; normal-mode wiring keeps its existing heading-regex check
  untouched). Heavily comment the marker mechanism (what/why).
• New .filetree.local.json (git-excluded) state file records: exact
  .git/info/exclude lines added, which local files were freshly created
  vs pre-existing (drives whole-file-delete vs strip-marked-span on
  uninstall).
• New /filetree:uninstall command, self-only-only: reads state file,
  strips marker-delimited sections (or deletes freshly-created files),
  removes the exact exclude lines added, deletes generated outputs
  (manifest, hash sidecar, .filetree.json), deletes the state file itself
  last. No-ops with a message if self_only isn't set.
• commit_guard / lint / update: unaffected, work unchanged (they operate
  on disk regardless of git-tracking status).

No more open questions — proceeding to implementation.